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The Nucleosome

The Nucleosome

Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...

The Nucleosome

The Nucleosome

DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...

The Nucleosome

The Nucleosome

DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...

Nucleosome Remodeling

Nucleosome Remodeling

Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...

The DNA Helix

The DNA Helix

Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...

The DNA Helix

The DNA Helix

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Related Experiment Video

Updated: Jun 18, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Base pair stacking in nucleosome DNA and bendability sequence pattern.

Edward N Trifonov¹

¹Genome Diversity Center, Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel. trifonov@research.haifa.ac.il

Journal of Theoretical Biology

|December 8, 2009

Summary

This summary is machine-generated.

This study reveals a DNA sequence pattern that optimizes nucleosome formation by minimizing base pair unstacking. This finding suggests a universal eukaryotic pattern for DNA bendability within nucleosomes.

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Area of Science:

Molecular Biology
Biophysics
Genetics

Background:

DNA wraps around histone proteins to form nucleosomes, a fundamental process in eukaryotic cells.
Nucleosome structure and DNA bending are crucial for gene regulation and DNA accessibility.
Understanding DNA deformation within nucleosomes is key to deciphering genome organization.

Purpose of the Study:

To identify the theoretical DNA sequence pattern that is most compatible with nucleosome formation.
To investigate the relationship between DNA base-pair stacking and nucleosome structure.
To propose a fundamental sequence pattern for eukaryotic nucleosome DNA bendability.

Main Methods:

Computational modeling of DNA base-pair stack orientations relative to the histone octamer.
Derivation of an optimal DNA sequence based on energetic principles of DNA deformation.
Comparison of the theoretical sequence with existing experimental data on nucleosome DNA.

Main Results:

A specific DNA sequence pattern was theoretically derived that minimizes DNA deformation during nucleosome assembly.
The derived sequence pattern shows significant consistency with experimentally observed DNA sequences in nucleosomes.
The results suggest that DNA sequence intrinsically influences nucleosome formation and stability.

Conclusions:

A fundamental DNA sequence pattern exists that dictates optimal nucleosome formation across eukaryotes.
DNA bendability and nucleosome compatibility are governed by basic biophysical principles of base-pair stacking.
This work provides a theoretical framework for understanding sequence-directed nucleosome organization.